PTPN13

Summary

PTPN13 (protein tyrosine phosphatase non-receptor type 13, HGNC:9646) is a protein-coding gene on chromosome 4q21.3, encoding Tyrosine-protein phosphatase non-receptor type 13 (Q12923). Tyrosine phosphatase which negatively regulates FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling.

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large intracellular protein. It has a catalytic PTP domain at its C-terminus and two major structural domains: a region with five PDZ domains and a FERM domain that binds to plasma membrane and cytoskeletal elements. This PTP was found to interact with, and dephosphorylate, Fas receptor and IkappaBalpha through the PDZ domains. This suggests it has a role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathways. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported.

Source: NCBI Gene 5783 — RefSeq curated summary.

At a glance

• Gene–disease (curated): bone marrow failure syndrome (Moderate, GenCC)
• GWAS associations: 7
• Clinical variants (ClinVar): 435 total
• Druggable target: yes
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 3 cancer types
• MANE Select transcript: NM_080683

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9646
Approved symbol	PTPN13
Name	protein tyrosine phosphatase non-receptor type 13
Location	4q21.3
Locus type	gene with protein product
Status	Approved
Aliases	PTP1E, PTP-BAS, PTPL1, PTP-BL
Ensembl gene	ENSG00000163629
Ensembl biotype	protein_coding
OMIM	600267
Entrez	5783

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 22 protein_coding, 2 retained_intron

ENST00000316707, ENST00000411767, ENST00000427191, ENST00000436978, ENST00000502971, ENST00000507902, ENST00000508063, ENST00000511105, ENST00000511467, ENST00000860769, ENST00000860770, ENST00000860771, ENST00000860772, ENST00000940451, ENST00000940452, ENST00000940453, ENST00000940454, ENST00000940455, ENST00000940456, ENST00000940457, ENST00000940458, ENST00000940459, ENST00000953522, ENST00000953523

RefSeq mRNA: 4 — MANE Select: NM_080683 NM_006264, NM_080683, NM_080684, NM_080685

CCDS: CCDS47093, CCDS47094, CCDS47095, CCDS47096

Canonical transcript exons

ENST00000411767 — 48 exons

Exon	Start	End
ENSE00001076725	86764593	86764724
ENSE00001076728	86769769	86769983
ENSE00001076729	86807560	86807897
ENSE00001076731	86809769	86809984
ENSE00001076736	86785848	86785936
ENSE00001076737	86770101	86770199
ENSE00001076740	86774373	86774531
ENSE00001076741	86766432	86766517
ENSE00001076747	86803709	86803857
ENSE00001076749	86772778	86772958
ENSE00001076752	86775442	86775652
ENSE00001076758	86796874	86796929
ENSE00001076761	86732592	86732766
ENSE00001076763	86767817	86767976
ENSE00001076767	86771171	86771535
ENSE00001216640	86799101	86799204
ENSE00001216712	86741634	86741816
ENSE00001216802	86775171	86775342
ENSE00001216927	86735594	86735746
ENSE00001216934	86734737	86734875
ENSE00001216943	86734303	86734456
ENSE00001325693	86762727	86763190
ENSE00001364834	86635252	86635371
ENSE00001364860	86672365	86672543
ENSE00001366520	86693587	86693674
ENSE00001368206	86750470	86750887
ENSE00001369928	86701241	86701801
ENSE00001371682	86732400	86732474
ENSE00001372823	86716530	86716625
ENSE00001377593	86717024	86717117
ENSE00001382188	86722212	86722434
ENSE00001387588	86689005	86689190
ENSE00001388101	86686710	86686775
ENSE00001390951	86744966	86745128
ENSE00001403980	86805279	86805369
ENSE00001406653	86753009	86753065
ENSE00001407850	86758678	86758785
ENSE00001415404	86780402	86780472
ENSE00001416845	86594315	86594789
ENSE00001417450	86811046	86811108
ENSE00001420498	86751027	86751124
ENSE00001421731	86758260	86758349
ENSE00001428369	86782201	86782262
ENSE00001797192	86785231	86785368
ENSE00001804791	86784465	86784558
ENSE00003460634	86765395	86765488
ENSE00003559640	86758942	86759073
ENSE00003845816	86814456	86815161

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 97.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.8890 / max 1049.0498, expressed in 1481 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
48670	15.8503	1442
48671	5.0386	1185

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
mucosa of paranasal sinus	UBERON:0005030	97.09	gold quality
urethra	UBERON:0000057	96.72	gold quality
penis	UBERON:0000989	96.47	gold quality
palpebral conjunctiva	UBERON:0001812	96.05	gold quality
pigmented layer of retina	UBERON:0001782	95.88	gold quality
upper arm skin	UBERON:0004263	95.86	gold quality
renal medulla	UBERON:0000362	95.64	gold quality
trigeminal ganglion	UBERON:0001675	95.33	gold quality
endometrium epithelium	UBERON:0004811	94.77	gold quality
gingival epithelium	UBERON:0001949	94.71	gold quality
gingiva	UBERON:0001828	94.59	gold quality
pharyngeal mucosa	UBERON:0000355	94.23	gold quality
calcaneal tendon	UBERON:0003701	94.03	gold quality
dorsal root ganglion	UBERON:0000044	93.73	gold quality
cervix squamous epithelium	UBERON:0006922	93.38	gold quality
upper leg skin	UBERON:0004262	93.31	gold quality
cervix epithelium	UBERON:0004801	93.28	gold quality
epithelium of nasopharynx	UBERON:0001951	93.11	gold quality
corpus callosum	UBERON:0002336	93.01	gold quality
skin of hip	UBERON:0001554	91.65	gold quality
choroid plexus epithelium	UBERON:0003911	91.65	gold quality
skin of abdomen	UBERON:0001416	91.62	gold quality
oral cavity	UBERON:0000167	91.25	gold quality
zone of skin	UBERON:0000014	91.22	gold quality
nasal cavity epithelium	UBERON:0005384	91.06	gold quality
skin of leg	UBERON:0001511	90.97	gold quality
tongue squamous epithelium	UBERON:0006919	90.78	gold quality
mammalian vulva	UBERON:0000997	90.77	gold quality
corpus epididymis	UBERON:0004359	90.64	gold quality
lower lobe of lung	UBERON:0008949	90.33	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	37.27
E-GEOD-130148	yes	12.76
E-CURD-112	no	2.99
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPB, CUX1, ETV6, EWSR1, FLI1, FOXC1, IRF8, NFKB1, NFKB, RELA, SPI1, STAT3, TP53

miRNA regulators (miRDB)

88 targeting PTPN13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4307	99.82	70.45	3374

Literature-anchored findings (GeneRIF, showing 40)

• Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL (PMID:11884147)
• expression and apoptosis induction in peripheral blood cells from liver graft (PMID:11959286)
• PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with peptide, RA-GEF-2, reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions (PMID:12095257)
• PTPL1/FAP-1 has a key role in the apoptotic process in human breast cancer cells independent of Fas but associated with an early inhibition of the insulin receptor substrate-1/phosphatidylinositol 3-kinase pathway (PMID:12354757)
• Shares a promoter region with the tightly linked gene encoding stress-activated protein kinase JNK3. (PMID:12436199)
• FAP-1 has a role in binding to, and consequently inhibition of, Fas export to the cell surface (PMID:12724420)
• specificity of interaction between the second PDZ domain of human protein tyrosine phosphatase1E (PDZ2) and a C-terminal peptide, ENEQVSAV, from the guanine nucleotide exchange factor RA-GEF-2 was investigated using FTIR spectroscopy and ESI-MS (PMID:12870871)
• PTPL1 binds to tandem-PH-domain-containing protein (TAPP)-1. (PMID:14516276)
• Data report the solution structure of the PDZ2 domain splicing variant of the protein tyrosine phosphatase PTP-Bas. (PMID:14596806)
• X-ray crystallographic analysis of the PTPL1 catalytic domain (PMID:15611135)
• We therefore report a novel transcriptional activation of a phosphatase involved in the oncogenesis of ESFT. (PMID:15782144)
• FAP-1 expression is often up-regulated in metastatic tumors, with a causal connection withNF-kappaB-dependent transcriptional regulation of FAP-1 gene expression. (PMID:16306044)
• FAP-1 could be inactivated during hepatocarcinogenesis, mainly attributed by allelic loss and promoter methylation. (PMID:16489062)
• The PTPN13 protein has proapoptotic functions and can fuction as TSGs to suppress tumorigenesis. (PMID:16572203)
• FAP-1 phosphatase activity could be responsible for NF-kappaB activation and resistance of SCCHN cells to Fas-mediated apoptosis. (PMID:16888780)
• use the second PDZ domain (PDZ2) of protein tyrosine phosphatase (PTP1E) as a model to study the energetics of peptide binding to a class I PDZ domain. (PMID:17240990)
• PTPN13/PTPL1 induces apoptosis through insulin receptor substrate-1 dephosphorylation (PMID:17638892)
• cellular PTPN13 inhibits Her2 activity by dephosphorylating the signal domain of Her2 and plays a role in attenuating invasiveness and metastasis of Her2 overactive tumors. (PMID:17982484)
• Frameshift mutation in the polyadenine tracts in both FLASH and PTPN13 genes is rare in colorectal carcinomas. Both FLASH and PTPN13 mutations in the polyadenine tracts may not have a crucial role in the pathogenesis of colorectal carcinomas. (PMID:18038312)
• The interferon consensus sequence-binding protein (ICSBP/IRF8) represses PTPN13 gene transcription in differentiating myeloid cells (PMID:18195016)
• erythrocyte CR1 ligation induces its clustering in complex with scaffolding protein FAP-1 (PMID:18684861)
• PTPL1 expression level is an independent prognostic indicator of favorable outcome for patients with breast cancer (PMID:19004008)
• PTPN13 SNPs were found to influence susceptibility to a wide spectrum of cancers. (PMID:19672627)
• PTPN13 phosphatase activity has a physiologically significant role in regulating MAP kinase signaling (PMID:19734941)
• polymorphisms in the PTPN13 coding region may have a role in susceptibility to squamous cell carcinoma of head and neck (PMID:19892796)
• Transfection of FAP-1 siRNA into SW480 cells silenced the expression of FAP-1 and consequently abolished the inhibitory function of Fas/FasL-mediated apoptosis pathway, thus increasing the efficacy of chemotherapy for colon carcinoma with oxaliplatin. (PMID:20039457)
• PTPL1 regulates breast cancer cell aggressiveness through direct inactivation of Src kinase. (PMID:20501847)
• FAP-1 was demonstrated to be responsible for the reduced sensitivity to CD95-mediated apoptosis in cells with inhibited miR-200. (PMID:20620960)
• X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand; very minor structural changes in PDZ2 accompany peptide binding (PMID:20839809)
• REVIEW: the alterations in expression and the genetic and epigenetic arguments supporting an oncogenic or an anti-oncogenic impact of PTPL1 (PMID:21235435)
• The Ret oncoprotein exerts opposing controls on Fap-1 and CD95, increasing Fap-1 expression and decreasing CD95 cell surface expression. (PMID:21741956)
• interaction between Tel and Tel-PdgfRbeta decreases Tel/Icsbp/Hdac3 binding to the PTPN13 cis element, resulting in increased transcription. (PMID:22262849)
• The PTPL1 is an important mediator of central cellular processes such as proliferation and invasion. (PMID:22274591)
• Data show that EphrinB1, a PTPN13 substrate, interacts with ErbB2, and Src kinase mediates EphrinB1 phosphorylation and subsequent MAP Kinase signaling. (PMID:22279592)
• CD95 signal transduction was not affected by FAP-1 expression in A818-6 monolayer cells; we found a polarisation-induced co-localisation of CD95 and FAP-1. (PMID:22364882)
• Studied the peptide binding induced dynamical changes at the side-chain level throughout the second PDZ domain of PTP1e, identifying as such the collection of residues involved in long-range communication. (PMID:23209399)
• Fap1-dependent inactivation of Gsk3beta and consequent stabilization of betacatenin in these cells. Consistent with this, Bcr-abl(+) cells exhibited a Fap1-dependent increase in betacatenin activity. (PMID:23519466)
• The loss of PTPL1 and PKC-delta expression in poorly differentiated, more aggressive human prostate cancers indicate that their absence could be related to apoptosis resistance and tumor progression. (PMID:23559010)
• PTPL1 dephosphorylates p85beta, promoting its binding to FBXL2 and degradation. (PMID:23604317)
• Low PTPN13 expression is associated with invasion and metastasis of lung squamous cell carcinoma. (PMID:23906871)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptpn13	ENSDARG00000103699
mus_musculus	Ptpn13	ENSMUSG00000034573
rattus_norvegicus	Ptpn13	ENSRNOG00000002061

Paralogs (35): PTPRN (ENSG00000054356), PTPRU (ENSG00000060656), PTPN3 (ENSG00000070159), PTPN21 (ENSG00000070778), PTPN18 (ENSG00000072135), PTPN23 (ENSG00000076201), PTPRH (ENSG00000080031), PTPRC (ENSG00000081237), PTPN4 (ENSG00000088179), PTPRS (ENSG00000105426), PTPRZ1 (ENSG00000106278), PTPN5 (ENSG00000110786), PTPN6 (ENSG00000111679), PTPRB (ENSG00000127329), PTPN12 (ENSG00000127947), PTPRE (ENSG00000132334), PTPRA (ENSG00000132670), PTPN22 (ENSG00000134242), PTPRF (ENSG00000142949), PTPN7 (ENSG00000143851), PTPRG (ENSG00000144724), PTPRJ (ENSG00000149177), PTPRO (ENSG00000151490), PTPN14 (ENSG00000152104), PTPRK (ENSG00000152894), PTPRR (ENSG00000153233), PTPRD (ENSG00000153707), PTPRN2 (ENSG00000155093), PTPN9 (ENSG00000169410), PTPRM (ENSG00000173482), PTPN2 (ENSG00000175354), PTPN11 (ENSG00000179295), PTPRT (ENSG00000196090), PTPN1 (ENSG00000196396), PTPN20 (ENSG00000204179)

Protein

Protein identifiers

Tyrosine-protein phosphatase non-receptor type 13 — Q12923 (reviewed: Q12923)

Alternative names: Fas-associated protein-tyrosine phosphatase 1, PTP-BAS, Protein-tyrosine phosphatase 1E, Protein-tyrosine phosphatase PTPL1

All UniProt accessions (3): Q12923, D6R9M4, D6R9X4

UniProt curated annotations — full annotation on UniProt →

Function. Tyrosine phosphatase which negatively regulates FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling. May regulate phosphoinositide 3-kinase (PI3K) signaling through dephosphorylation of PIK3R2.

Subunit / interactions. Interacts (via the first PDZ domain) with PLEKHA1 and PLEKHA2. Interacts (via the second PDZ domain) with TNFRSF6 (Fas receptor) (via C-terminus). Interacts (via the second PDZ domain) with TRIP6 (via the third LIM domain and C-terminus). Interacts (via the third PDZ domain) with NGFR (via C-terminal SVP motif) and PKN2 (via C-terminus). Interacts (via the second or fourth PDZ domains) with PDLIM4 (via C-terminus only or via combined C-terminus and LIM domain, but not LIM domain only). Found in a complex with PDLIM4 and TRIP6. Interacts with PDLIM4; this interaction results in dephosphorylation of SRC ‘Tyr-419’ by this protein leading to its inactivation. Interacts with BRD7. Interacts with RAPGEF6. Interacts with ARHGAP29. Interacts with PIK3R2; dephosphorylates PIK3R2. Interacts with FBXL2. Interacts (via the FERM domain) with ENTR1. Found in a complex with ENTR1, PTPN13 and GIT1.

Subcellular location. Cytoplasm. Cytoskeleton. Nucleus. Cell projection. Lamellipodium.

Tissue specificity. Expressed in keratinocytes (at protein level). Present in most tissues with the exception of the liver and skeletal muscle. Most abundant in lung, kidney and fetal brain.

Miscellaneous. May be due to a competing donor splice site.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.

Isoforms (4)

UniProt ID	Names	Canonical?
Q12923-1	1	yes
Q12923-2	2
Q12923-3	3
Q12923-4	4

RefSeq proteins (4): NP_006255, NP_542414, NP_542415, NP_542416 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000242	PTP_cat	Domain
IPR000299	FERM_domain	Domain
IPR000387	Tyr_Pase_dom	Domain
IPR001478	PDZ	Domain
IPR003595	Tyr_Pase_cat	Domain
IPR011019	KIND_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR012153	PTPN13	Family
IPR014352	FERM/acyl-CoA-bd_prot_sf	Homologous_superfamily
IPR018979	FERM_N	Domain
IPR018980	FERM_PH-like_C	Domain
IPR019748	FERM_central	Domain
IPR019749	Band_41_domain	Domain
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR035963	FERM_2	Homologous_superfamily
IPR036034	PDZ_sf	Homologous_superfamily
IPR052074	NonRcpt_TyrProt_Phosphatase	Family

Pfam: PF00102, PF00373, PF00595, PF09379, PF09380, PF16599

Enzyme classification (BRENDA):

• EC 3.1.3.48 — protein-tyrosine-phosphatase (BRENDA: 59 organisms, 501 substrates, 1326 inhibitors, 270 Km, 165 kcat entries)

Substrate kinetics (BRENDA)

70 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
4-NITROPHENYL PHOSPHATE	0.0008–148	84
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE	0.0039–0.862	27
P-NITROPHENYL PHOSPHATE	0.0024–10	20
DADEPYLIPQQG	0.0003–0.1	12
PHOSPHOTYROSINE	0.012–30	11
LYSOZYME	0.0003–0.012	5
MYELIN BASIC PROTEIN	0.0001–0.022	5
ACETYL-DADEPY-NH2	0.0228–0.219	4
ACETYL-DADEPYL-NH2	1.1–97.5	4
4,6,8-TRIMETHYL-2-OXO-2H-CHROMEN-7-YL DIHYDROGEN	0.02–0.156	3
SASASPYSASA	0.53–2.3	3
1-NAPHTHYL PHOSPHATE	1.19–1.88	2
3,6-FLUORESCEIN DIPHOSPHATE	15–19	2
4-METHYLUMBELLIFERYL PHOSPHATE	0.953–2.41	2
BOVINE SERUM ALBUMIN	0.0001–0.0003	2

Catalyzed reactions (Rhea), 1 shown:

• O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)

UniProt features (123 total): strand 23, helix 16, compositionally biased region 12, sequence conflict 12, region of interest 11, modified residue 11, mutagenesis site 11, domain 8, sequence variant 7, turn 3, binding site 3, splice variant 3, chain 1, coiled-coil region 1, active site 1

Structure

Experimental structures (PDB)

12 structures.

PDB	Method	Resolution (Å)
3LNY	X-RAY DIFFRACTION	1.3
5GLJ	X-RAY DIFFRACTION	1.6
3LNX	X-RAY DIFFRACTION	1.64
1WCH	X-RAY DIFFRACTION	1.85
7XTY	X-RAY DIFFRACTION	2.1
1D5G	SOLUTION NMR
1Q7X	SOLUTION NMR
2M0Z	SOLUTION NMR
2M10	SOLUTION NMR
3PDZ	SOLUTION NMR
7QCX	SOLUTION NMR
7QCY	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q12923-F1	60.36	0.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 2408 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (3): 2378; 2408–2414; 2452

Post-translational modifications (11): 240, 301, 302, 890, 897, 908, 911, 914, 1029, 1033, 1085

Mutagenesis-validated functional residues (11):

Position	Phenotype
2154	no effect on substrate affinity.
2205	no effect on substrate affinity.
2221	reduces substrate affinity 2 fold.
2307	reduces substrate affinity 7 fold.
2408	loss of catalytic activity.
2444	loss of catalytic activity.
2444	reduces substrate affinity 7 fold.
2444	strongly decreases catalytic activity.
2448	reduces substrate affinity 2 fold.
2449	loss of catalytic activity.
2474	no effect on substrate affinity.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-1660499	Synthesis of PIPs at the plasma membrane
R-HSA-9008059	Interleukin-37 signaling
R-HSA-9696264	RND3 GTPase cycle
R-HSA-9696270	RND2 GTPase cycle
R-HSA-9696273	RND1 GTPase cycle

MSigDB gene sets: 315 (showing top): GOBP_REGULATION_OF_PHOSPHORYLATION, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_SYNAPSE_ASSEMBLY, GOZGIT_ESR1_TARGETS_DN, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_NEGATIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, MARTINEZ_RB1_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_CELLULAR_RESPONSE_TO_TOXIC_SUBSTANCE

GO Biological Process (8): negative regulation of protein phosphorylation (GO:0001933), protein dephosphorylation (GO:0006470), peptidyl-tyrosine dephosphorylation (GO:0035335), regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051896), cellular response to toxic substance (GO:0097237), negative regulation of excitatory synapse assembly (GO:1904890), dephosphorylation (GO:0016311), regulatory ncRNA-mediated gene silencing (GO:0031047)

GO Molecular Function (5): protein tyrosine phosphatase activity (GO:0004725), phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), lamellipodium (GO:0030027), cell body (GO:0044297), extracellular exosome (GO:0070062), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
RHO GTPase cycle	3
PI Metabolism	1
Interleukin-1 family signaling	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
regulation of protein phosphorylation	1
protein phosphorylation	1
negative regulation of protein modification process	1
negative regulation of phosphorylation	1
dephosphorylation	1
protein modification process	1
protein dephosphorylation	1
phosphatidylinositol 3-kinase/protein kinase B signal transduction	1
regulation of intracellular signal transduction	1
response to toxic substance	1
cellular response to chemical stimulus	1
negative regulation of synapse assembly	1
excitatory synapse assembly	1
regulation of excitatory synapse assembly	1
phosphate-containing compound metabolic process	1
negative regulation of gene expression	1
phosphoprotein phosphatase activity	1
phosphatidylinositol 3-kinase binding	1
phosphatase activity	1
catalytic activity, acting on a protein	1
binding	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
membrane	1
cell periphery	1
cell leading edge	1
plasma membrane bounded cell projection	1
extracellular vesicle	1

Protein interactions and networks

STRING

1457 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTPN13	FAS	P25445	923
PTPN13	ARHGAP29	Q52LW3	861
PTPN13	EFNB1	P98172	825
PTPN13	RAPGEF6	Q8TEU7	817
PTPN13	EFNB2	P52799	764
PTPN13	EFNB3	Q15768	725
PTPN13	CAV1	Q03135	713
PTPN13	SRC	P12931	708
PTPN13	APC	P25054	682
PTPN13	PRY	O14603	682
PTPN13	PTPRG	P23470	633
PTPN13	ENTR1	Q96C92	630
PTPN13	PTS	Q03393	621
PTPN13	EPHB4	P54760	600
PTPN13	FADD	Q13158	592
PTPN13	PDCD10	Q9BUL8	592

IntAct

654 interactions, top by confidence:

A	B	Type	Score
PDCD10	STK25	psi-mi:“MI:0914”(association)	0.980
YWHAB	PIK3C2A	psi-mi:“MI:0914”(association)	0.800
RNF146	TNKS	psi-mi:“MI:0914”(association)	0.790
RAPGEF1	CRKL	psi-mi:“MI:0914”(association)	0.720
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
E	PTPN13	psi-mi:“MI:0915”(physical association)	0.670
PTPN13	E	psi-mi:“MI:0915”(physical association)	0.670
E	PTPN13	psi-mi:“MI:0407”(direct interaction)	0.670
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
APC	PTPN13	psi-mi:“MI:0407”(direct interaction)	0.620
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:2364”(proximity)	0.610
FAS	PTPN13	psi-mi:“MI:0915”(physical association)	0.590
E	PTPN13	psi-mi:“MI:0915”(physical association)	0.590
SLC16A3	CASK	psi-mi:“MI:0914”(association)	0.590
YWHAE	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAZ	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
CFTR	PTPN13	psi-mi:“MI:0407”(direct interaction)	0.570

BioGRID (243): PTPN13 (Affinity Capture-MS), PTPN13 (Affinity Capture-MS), PTPN13 (Affinity Capture-MS), PTPN13 (Affinity Capture-MS), PTPN13 (Co-fractionation), PTPN13 (Proximity Label-MS), PTPN13 (Proximity Label-MS), PTPN13 (Affinity Capture-MS), PTPN13 (Two-hybrid), PLEKHA1 (Affinity Capture-MS), STXBP4 (Affinity Capture-MS), PTPN13 (Proximity Label-MS), PTPN13 (Affinity Capture-MS), PTPN13 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS)

ESM2 similar proteins: A0A571BF63, A0A8M9QN10, A0JMA8, A1A535, A1A5P5, A1L1K1, A2AVJ5, A7YDW0, B3MJV4, B4MV81, O00443, O08576, O17237, Q0V9V7, Q12923, Q14D04, Q17QK1, Q1LYM3, Q2NKQ1, Q3UGY8, Q59EK9, Q5EB20, Q5JWR5, Q5PQS3, Q5R565, Q5RAY1, Q5TH69, Q5U245, Q5U3W3, Q5XHG1, Q61194, Q61QK6, Q64512, Q6ING4, Q6MZQ0, Q6ZUJ8, Q7Z3E5, Q803Q4, Q80U12, Q8BPQ7

Diamond homologs: A0A140LI67, A5PKA5, A7UA95, E1JIT7, O14910, O15018, O19132, O35274, O35867, O35889, O62666, O62674, O62675, O62676, O62677, O62678, O88951, O88952, P11434, P29475, P29476, P31016, P51140, P55196, P57105, P78352, Q07436, Q0P5F3, Q12923, Q14005, Q29498, Q2KIB6, Q32LM6, Q3T0C9, Q3UHD6, Q4KL35, Q5F425, Q5RAA5, Q62108, Q64512

SIGNOR signaling

14 interactions.

A	Effect	B	Mechanism
PTPN13	down-regulates	INSR	dephosphorylation
PTPN13	down-regulates	PDCD10	dephosphorylation
PTPN13	“down-regulates activity”	STK25	dephosphorylation
PTPN13	“up-regulates quantity by stabilization”	NFKBIA	dephosphorylation
PTPN13	“down-regulates activity”	PDCD10	dephosphorylation
PTPN13	“up-regulates activity”	EFNB1	dephosphorylation
PTPN13	“down-regulates activity”	ABL1	dephosphorylation
PTPN13	“down-regulates activity”	IRS1	dephosphorylation
PTPN13	“down-regulates activity”	ERBB2	dephosphorylation
PTPN13	“down-regulates activity”	SRC	dephosphorylation
PTPN13	“down-regulates activity”	TRIP6	dephosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 188 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	8	42.3×	1e-09
Activation of BAD and translocation to mitochondria	7	42.0×	2e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	37.0×	4e-08
Activation of BH3-only proteins	7	27.4×	4e-07
RHO GTPases activate PKNs	8	20.0×	4e-07
EPHA-mediated growth cone collapse	6	18.0×	4e-05
Intrinsic Pathway for Apoptosis	7	16.1×	1e-05
FOXO-mediated transcription	6	15.9×	7e-05

GO biological processes:

GO term	Partners	Fold	FDR
ephrin receptor signaling pathway	8	16.6×	4e-05
regulation of GTPase activity	5	15.4×	3e-03
protein targeting	6	13.2×	1e-03
positive regulation of protein localization to plasma membrane	7	11.5×	1e-03
Ras protein signal transduction	7	8.7×	3e-03
positive regulation of neuron projection development	9	7.4×	1e-03
cell surface receptor protein tyrosine kinase signaling pathway	7	7.3×	5e-03
intracellular protein localization	11	6.9×	4e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 3 cancer types — BLCA, PANCREAS, UCEC.

Clinical variants and AI predictions

ClinVar

435 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	348
Likely benign	25
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

7392 predictions. Top by Δscore:

Variant	Effect	Δscore
4:86603859:G:GT	donor_gain	1.0000
4:86603874:GCCAT:G	donor_gain	1.0000
4:86635372:G:A	donor_loss	1.0000
4:86635373:T:A	donor_loss	1.0000
4:86672336:T:G	acceptor_gain	1.0000
4:86672342:A:AG	acceptor_gain	1.0000
4:86672342:ATTTT:A	acceptor_gain	1.0000
4:86672346:T:TA	acceptor_gain	1.0000
4:86672347:G:A	acceptor_gain	1.0000
4:86672352:A:AG	acceptor_gain	1.0000
4:86672356:A:AG	acceptor_gain	1.0000
4:86672357:C:G	acceptor_gain	1.0000
4:86672358:A:AG	acceptor_gain	1.0000
4:86672359:A:G	acceptor_gain	1.0000
4:86672539:AAAAG:A	donor_loss	1.0000
4:86672540:AAAGG:A	donor_loss	1.0000
4:86672541:AAG:A	donor_loss	1.0000
4:86672542:AG:A	donor_loss	1.0000
4:86672543:GG:G	donor_loss	1.0000
4:86672545:T:A	donor_loss	1.0000
4:86686776:G:GG	donor_gain	1.0000
4:86686781:T:G	donor_gain	1.0000
4:86688998:T:G	acceptor_gain	1.0000
4:86689004:GCCT:G	acceptor_gain	1.0000
4:86689118:G:GT	donor_gain	1.0000
4:86693586:GACA:G	acceptor_gain	1.0000
4:86693673:AGG:A	donor_loss	1.0000
4:86693674:GGT:G	donor_loss	1.0000
4:86693675:G:GC	donor_loss	1.0000
4:86693676:T:G	donor_loss	1.0000

AlphaMissense

16339 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:86758951:T:C	L1144S	1.000
4:86809811:T:A	W2376R	1.000
4:86809811:T:C	W2376R	1.000
4:86635338:A:C	S28R	0.999
4:86635340:T:A	S28R	0.999
4:86635340:T:G	S28R	0.999
4:86741787:T:A	W820R	0.999
4:86741787:T:C	W820R	0.999
4:86759038:T:C	L1173P	0.999
4:86764720:T:A	V1382D	0.999
4:86766441:T:A	V1418D	0.999
4:86769814:G:A	G1512E	0.999
4:86769817:T:C	F1513S	0.999
4:86807664:G:A	G2284R	0.999
4:86807664:G:C	G2284R	0.999
4:86809910:A:C	S2409R	0.999
4:86809912:T:A	S2409R	0.999
4:86809912:T:G	S2409R	0.999
4:86734362:T:A	W640R	0.998
4:86734362:T:C	W640R	0.998
4:86745015:T:C	F846S	0.998
4:86758681:T:C	F1106S	0.998
4:86758956:T:C	S1146P	0.998
4:86766438:G:C	R1417P	0.998
4:86766450:T:A	V1421D	0.998
4:86766488:G:C	A1434P	0.998
4:86767827:T:C	L1447P	0.998
4:86769813:G:A	G1512R	0.998
4:86769813:G:C	G1512R	0.998
4:86769816:T:C	F1513L	0.998

dbSNP variants (sampled 300 via entrez): RS1000009579 (4:86698101 T>A), RS1000011765 (4:86747804 C>A,T), RS1000057006 (4:86624765 A>T), RS1000070988 (4:86641017 G>A,T), RS1000072722 (4:86606120 G>A), RS1000076754 (4:86772436 C>G), RS10000891 (4:86747374 G>A), RS1000096642 (4:86755143 C>A), RS10001010 (4:86747525 G>A), RS1000116504 (4:86701542 C>T), RS1000122749 (4:86714324 T>G), RS1000144132 (4:86598337 G>A,T), RS1000148591 (4:86609009 A>G), RS1000162764 (4:86668337 A>G,T), RS1000164203 (4:86741535 T>C)

Disease associations

OMIM: gene MIM:600267 | disease phenotypes: MIM:156000, MIM:192500

GenCC curated gene-disease

Disease	Classification	Inheritance
bone marrow failure syndrome	Moderate	Autosomal recessive

Mondo (3): Meniere disease (MONDO:0007972), familial long QT syndrome (MONDO:0019171), bone marrow failure syndrome (MONDO:0000159)

Orphanet (3): Romano-Ward syndrome (Orphanet:101016), Congenital long QT syndrome (Orphanet:768), NON RARE IN EUROPE: Menière disease (Orphanet:45360)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003476_4	Eyebrow thickness	2.000000e-06
GCST003861_1	Kidney disease (end stage renal disease vs normoalbuminuria) in type 1 diabetes	6.000000e-06
GCST003862_1	Kidney disease (end stage renal disease vs non-end stage renal disease) in type 1 diabetes	2.000000e-06
GCST007467_8	Word spelling	6.000000e-06
GCST010083_56	Hemoglobin levels	1.000000e-08
GCST011541_4	Tinnitus	2.000000e-07
GCST90000025_272	Appendicular lean mass	6.000000e-23

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005301	reading and spelling ability
EFO:0004509	hemoglobin measurement
EFO:0004980	appendicular lean mass

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008575	Meniere Disease	C09.218.568.217.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2976 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

17 potent at pChembl≥5 of 29 total, top 17 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.41	IC50	390	nM	CHEMBL2396718
6.22	IC50	600	nM	CHEMBL50878
5.89	IC50	1300	nM	CHEMBL2316902
5.80	IC50	1600	nM	CHEMBL2316907
5.72	IC50	1900	nM	CHEMBL2316906
5.66	IC50	2200	nM	CHEMBL3985776
5.55	IC50	2800	nM	CHEMBL3918902
5.54	IC50	2900	nM	CHEMBL2396719
5.37	IC50	4300	nM	CHEMBL3979554
5.36	IC50	4400	nM	CHEMBL51579
5.33	IC50	4700	nM	CHEMBL417727
5.25	IC50	5600	nM	CHEMBL3909342
5.19	IC50	6500	nM	CHEMBL3900333
5.16	IC50	7000	nM	CHEMBL51314
5.13	IC50	7400	nM	CHEMBL3899171
5.00	IC50	9900	nM	CHEMBL3908861
5.00	IC50	9900	nM	CHEMBL50347

PubChem BioAssay actives

18 with measured affinity, of 88 total; 18 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
3-[2-(3-chlorophenyl)ethynyl]-6-hydroxy-2-[4-[2-oxo-2-(propylamino)ethoxy]phenyl]-1-benzofuran-5-carboxylic acid	755774: Inhibition of recombinant FAP-1 (unknown origin) using pNPP as substrate by spectrophotometric analysis	ic50	0.3900	uM
N-(9,10-dioxophenanthren-2-yl)-2-fluorobenzamide	71463: Inhibitory concentration against FAP-1 pNPP	ic50	0.6000	uM
6-hydroxy-2-phenyl-3-[2-[3-(trifluoromethyl)phenyl]ethynyl]-1-benzofuran-5-carboxylic acid	725031: Inhibition of FAP1 (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysis	ic50	1.3000	uM
6-hydroxy-2-phenyl-3-[2-[4-(trifluoromethoxy)phenyl]ethynyl]-1-benzofuran-5-carboxylic acid	725031: Inhibition of FAP1 (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysis	ic50	1.6000	uM
3-[2-(3,5-difluorophenyl)ethynyl]-6-hydroxy-2-phenyl-1-benzofuran-5-carboxylic acid	725031: Inhibition of FAP1 (unknown origin) expressed in Escherichia coli using pNPP substrate after 5 mins by spectrophotometric analysis	ic50	1.9000	uM
2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxy-1-phenothiazin-10-ylethanone	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	2.2000	uM
2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxy-N-(4-phenylphenyl)acetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	2.8000	uM
3-[2-(3-chlorophenyl)ethynyl]-2-[4-[2-(cyclopropylamino)-2-oxoethoxy]phenyl]-6-hydroxy-1-benzofuran-5-carboxylic acid	755774: Inhibition of recombinant FAP-1 (unknown origin) using pNPP as substrate by spectrophotometric analysis	ic50	2.9000	uM
(5Z)-3-(3-chlorophenyl)-5-[(4-hydroxy-3-methoxy-5-nitrophenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one	1799621: PTP Assay from Article 10.1002/cbic.200600287: “Cellular inhibition of protein tyrosine phosphatase 1B by uncharged thioxothiazolidinone derivatives.”	ic50	3.7000	uM
N-[2-(2,4-dichlorophenyl)ethyl]-2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxyacetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	4.3000	uM
methyl 4-[(9,10-dioxophenanthren-1-yl)amino]-4-oxobutanoate	71463: Inhibitory concentration against FAP-1 pNPP	ic50	4.4000	uM
2-aminophenanthrene-9,10-dione	71466: Inhibitory concentration against FAP-1 using pNPP as substrate	ic50	4.7000	uM
N-(9H-fluoren-9-yl)-2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxyacetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	5.6000	uM
2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxy-N-(4-propan-2-ylphenyl)acetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	6.5000	uM
N-(9,10-dioxophenanthren-2-yl)-2,2-dimethylpropanamide	71463: Inhibitory concentration against FAP-1 pNPP	ic50	7.0000	uM
N-(1-adamantyl)-2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxyacetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	7.4000	uM
methyl 8-[(9,10-dioxophenanthren-2-yl)amino]-8-oxooctanoate	71463: Inhibitory concentration against FAP-1 pNPP	ic50	9.9000	uM
N-(1,3-benzothiazol-2-yl)-2-[6-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-7-hydroxynaphthalen-2-yl]oxyacetamide	1322861: Inhibition of recombinant FAP1 (unknown origin) using pNPP as substrate by spectrophotometric method	ic50	9.9000	uM

CTD chemical–gene interactions

64 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	3
Estradiol	affects cotreatment, increases expression, decreases expression	3
bisphenol A	decreases methylation, increases expression	2
potassium chromate(VI)	affects cotreatment, decreases expression, increases expression	2
(+)-JQ1 compound	increases expression	2
Arsenic	decreases expression, increases abundance, affects cotreatment	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Cadmium Chloride	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
urushiol	increases expression	1
methylmercuric chloride	decreases expression, increases expression	1
triphenyl phosphate	affects expression	1
glycidyl methacrylate	increases expression	1
sodium arsenate	decreases expression, increases abundance	1
terbufos	increases methylation	1
arsenite	affects binding, decreases reaction	1
doxifluridine	decreases response to substance	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
LY 117018	increases expression	1
cupric oxide	decreases expression	1
1-UFT protocol	decreases response to substance	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
arsenic disulfide	decreases methylation	1
glycidamide	decreases expression	1
chromium hexavalent ion	affects expression	1

ChEMBL screening assays

23 unique, capped per target: 22 binding, 1 admet

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1070017	Binding	Inhibition of FAP1 expressed in Escherichia coli assessed as inhibition of p-nitrophenyl phosphate hydrolysis at pH 7 by spectrophotometry	Salicylic acid based small molecule inhibitor for the oncogenic Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2). — J Med Chem
CHEMBL4626300	ADMET	Inhibition of FAP1 (unknown origin) expressed in Escherichia coli BL21 using p-nitrophenyl phosphate as substrate measured after 30 mins by UV-vis spectrophotometric method	Highly Potent and Selective N-Aryl Oxamic Acid-Based Inhibitors for Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. — J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2CS	Abcam HeLa PTPN13 KO	Cancer cell line	Female
CVCL_D7YY	Ubigene A-549 PTPN13 KO	Cancer cell line	Male

Clinical trials (associated diseases)

128 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT01574313	PHASE4	COMPLETED	Effect of Stellate Ganglion Block on Meniere’s Disease
NCT02529475	PHASE4	TERMINATED	Evaluation of Inner Ear and Brain Structures With Contrast-enhanced MRI in Healthy Subjects (HYDROPS)
NCT04815187	PHASE4	ACTIVE_NOT_RECRUITING	Repurposed Use of Allergic Rhinitis and Allergic Asthma Drug to Reduce Vertigo and Hearing Loss in Meniere’s Disease
NCT02513940	PHASE4	COMPLETED	Influence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883	PHASE4	COMPLETED	Reducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100	PHASE4	UNKNOWN	Novel Form of Acquired Long QT Syndrome
NCT04675788	PHASE4	COMPLETED	Novel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT00774527	PHASE3	COMPLETED	Comparison of Cy-Atg Vs Cy-Flu-Atg for the Conditioning Therapy in Allo-HCT
NCT02393508	PHASE3	UNKNOWN	The Impact of Red Cell Age on Product Utilization in the Chronically Transfused Outpatient Population
NCT06940570	PHASE3	SUSPENDED	Methadone as an Alternative Treatment for Children Underdoing HSCT
NCT03664674	PHASE3	COMPLETED	Phase 3 Study of OTO-104 in Subjects With Unilateral Meniere’s Disease
NCT04677972	PHASE3	COMPLETED	SPI-1005 for the Treatment of Meniere’s Disease
NCT05851508	PHASE3	RECRUITING	The Effecttiveness of Intratympanic Methylprednisolon Injections Compared to Placebo in the Treatment of Vertigo Attacks in Meniere’s Disease
NCT01050439	PHASE2	TERMINATED	Unrelated Donor Transplant for Malignant and Non-Malignant Disorders
NCT01596699	PHASE2	TERMINATED	Pilot Trial of Clofarabine Added to Standard Busulfan and Fludarabine for Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation
NCT01757145	PHASE2	UNKNOWN	Eltrombopag for Enhancing Platelet Engraftment in Adult Patients Undergoing Cord Blood Transplantation
NCT02224872	PHASE2	COMPLETED	Transplantation of Partially Mismatched Related or Matched Unrelated Bone Marrow for Patients With Refractory Severe Aplastic Anemia
NCT02277639	PHASE2	COMPLETED	Reduced Intensity Conditioning Using CD3+/CD19+ Depletion for Non Malignant Transplantable Diseases
NCT02349906	PHASE2	COMPLETED	Treosulfan-based Versus Busulfan-based Conditioning in Paediatric Patients With Non-malignant Diseases
NCT02722668	PHASE2	COMPLETED	UCB Transplant for Hematological Diseases Using a Non Myeloablative Prep
NCT04356469	PHASE2	RECRUITING	TCR Alpha Beta T-cell Depleted Haploidentical HCT in the Treatment of Non-Malignant Hematological Disorders in Children
NCT04558736	PHASE2	RECRUITING	Haploidentical HCT for Severe Aplastic Anemia
NCT04965597	PHASE2	COMPLETED	Treosulfan-Based Conditioning Regimen Before a Blood or Bone Marrow Transplant for the Treatment of Bone Marrow Failure Diseases (BMT CTN 1904)
NCT05420350	PHASE2	UNKNOWN	Lamotrigine and Bupropion for Meniere’s Disease
NCT06544434	PHASE2	RECRUITING	Laser Acupuncture for Meniere Disease
NCT01648205	PHASE2	COMPLETED	Long-term Efficacy Study of Sodium Channel Blocker in LQT3 Patients
NCT02412709	PHASE2	UNKNOWN	Long QT Syndrome Screening in Newborns
NCT04581408	PHASE2	COMPLETED	Mutation-specific Therapy for the Long QT Syndrome
NCT07585136	PHASE1	NOT_YET_RECRUITING	Stem Cell Mobilization and Apheresis for Life-threatening Blood Disorders
NCT04674735	PHASE1	WITHDRAWN	Safety of APSLXR in Patients Presenting Vertigo of Vestibular Origin or Meniere’s Disease
NCT00316459	PHASE1	COMPLETED	Study Evaluating the Effects of Multiple Oral Doses of ERB-041 on Cardiac Repolarization in Healthy Subjects
NCT01849003	PHASE1	COMPLETED	Study of the Effect of GS-6615 in Subjects With LQT-3
NCT02365532	PHASE1	COMPLETED	Effect of Oral GS-6615 on Dofetilide-Induced QT Prolongation, Safety, and Tolerability in Healthy Adults
NCT02412098	PHASE1	COMPLETED	Pharmacokinetics of Eleclazine in Adults With Normal and Impaired Hepatic Function
NCT02441829	PHASE1	COMPLETED	Pharmacokinetics of Eleclazine in Adults With Normal and Impaired Renal Function
NCT05759962	PHASE1	COMPLETED	Phase 1 Study of LQT-1213 in Healthy Adults
NCT01419704	PHASE1/PHASE2	WITHDRAWN	Phase I/II Pilot Study of Mixed Chimerism to Treat Hemoglobinopathies
NCT01966367	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	CD34+ (Non-Malignant) Stem Cell Selection for Patients Receiving Allogeneic Stem Cell Transplantation
NCT02055456	PHASE1/PHASE2	COMPLETED	Nandrolone Decanoate in the Treatment of Telomeropathies
NCT02337595	PHASE1/PHASE2	COMPLETED	Memory T-cell Infusion to Improve Immunity After TCR-alpha/Beta Depleted Hematopoietic Stem Cell Transplantation